bioinfo-skills

B. de Medeiros' Claude Skills Collection

Custom Claude skills for enhanced reasoning, bioinformatics, accounting, and natural history museum workflows. Each skill is a self-contained module bundled into installable plugins.

Available Plugins and Skills

general-skills

Skill	Description
extract-from-pdfs	8-step pipeline for extracting structured data from scientific PDFs using Claude's vision. Supports abstract filtering (Ollama/Haiku/Sonnet), external validation (GBIF, WFO, GeoNames, PubChem, NCBI), and export to multiple formats. Docs →
document-ocr	Converts scanned PDFs and document images into clean Markdown using docling for layout (figures, tables, reading order) plus a vision-language OCR model. Preserves multi-column order, diacritics, and figures. Supports local vLLM/Ollama and cloud vision APIs (OpenAI, Anthropic). Docs →
accounting	Processes procurement card receipts, tracks expenses in Google Sheets, reconciles records, and generates entertainment supplement tables. Docs →
lab-ordering	Places lab supply orders from member requests. Routes by request header to Amazon Business, the Pritzker Lab Google Form, or a direct vendor; stages the cart/form and stops for human review before any purchase. Docs →

bioinfo-skills

Skill	Description
phylo-from-buscos	Generates phylogenomic workflows from genome assemblies using BUSCO/compleasm single-copy orthologs. Supports NCBI accessions, multiple schedulers (SLURM, PBS, local), concatenated and coalescent phylogenies. Docs →
biogeobears	Sets up BioGeoBEARS biogeographic analyses in R. Validates inputs, generates RMarkdown scripts, compares DEC/DIVALIKE/BAYAREALIKE models, and produces publication-ready ancestral range visualizations. Docs →

museum-skills

Skill	Description
emu-bulk-upload	Helps FMNH entomology curators bulk upload specimen data to the Emu database. Matches localities to existing records, creates new site records, and generates formatted upload tables. Docs →

Installation

Claude Code — CLI, VS Code, or JetBrains (Recommended)

These instructions work the same way in:

• Claude Code CLI — type commands directly in the terminal
• VS Code — type commands in the Claude Code chat panel (or use /plugins to open the visual manager)
• JetBrains IDEs — type commands in the Claude Code panel

Step 1: Add the marketplace

You only need to do this once:

/plugin marketplace add brunoasm/my_claude_skills

Step 2: Install the plugins you need

Install all plugins:

/plugin install general-skills@brunoasm/my_claude_skills
/plugin install bioinfo-skills@brunoasm/my_claude_skills
/plugin install museum-skills@brunoasm/my_claude_skills

Or install only the ones you want — each plugin is independent.

Install from a local clone

git clone https://github.com/brunoasm/my_claude_skills.git
cd my_claude_skills

Then in Claude Code:

/plugin marketplace add .
/plugin install general-skills@.

Scope options

When installing, Claude Code will ask you to choose a scope:

• User — available in all your projects
• Project — shared with collaborators via .claude/settings.json
• Local — only you, only this repo

Claude.ai (Web)

1. Download the zip file for the desired skill from releases
2. Go to Claude.ai Settings > Capabilities > Skills
3. Click Upload Skill and select the ZIP file
4. Enable the skill

Resources

• Claude Code Plugins Documentation
• Claude Code Skills Documentation
• Claude.ai